Geographical Gradient of the eIF4E Alleles Conferring Resistance to Potyviruses in Pea (Pisum) Germplasm
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{"title"=>"Geographical gradient of the eif4ealleles conferring resistance to potyviruses in pea (pisum) germplasm", "type"=>"journal", "authors"=>[{"first_name"=>"Eva", "last_name"=>"Konečná", "scopus_author_id"=>"57193601260"}, {"first_name"=>"Dana", "last_name"=>"Šafářová", "scopus_author_id"=>"24333124500"}, {"first_name"=>"Milan", "last_name"=>"Navrátil", "scopus_author_id"=>"35305561700"}, {"first_name"=>"Pavel", "last_name"=>"Hanáček", "scopus_author_id"=>"6508388286"}, {"first_name"=>"Clarice", "last_name"=>"Coyne", "scopus_author_id"=>"7005683811"}, {"first_name"=>"Andrew", "last_name"=>"Flavell", "scopus_author_id"=>"7006591691"}, {"first_name"=>"Margarita", "last_name"=>"Vishnyakova", "scopus_author_id"=>"6603209207"}, {"first_name"=>"Mike", "last_name"=>"Ambrose", "scopus_author_id"=>"7006804917"}, {"first_name"=>"Robert", "last_name"=>"Redden", "scopus_author_id"=>"7003296791"}, {"first_name"=>"Petr", "last_name"=>"Smýkal", "scopus_author_id"=>"6603455441"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84897494489", "pui"=>"372754366", "sgr"=>"84897494489", "pmid"=>"24609094", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0090394"}, "id"=>"7be1536b-1065-39cc-8a6b-e5e2cc4eb6bc", "abstract"=>"BACKGROUND: The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the eIF4E gene to identify novel genetic diversity.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Germplasm of 2803 pea accessions was screened for eIF4E intron 3 length polymorphism, resulting in the detection of four eIF4E(A-B-C-S) variants, whose distribution was geographically structured. The eIF4E(A) variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, eIF4E(B), was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The eIF4E(C) variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The eIF4E(S) variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (eIF4E(A-1-2-3-4-5-6-7), eIF4E(B-1), eIF4E(C-2)) conferred resistance to the P1 PSbMV pathotype.\\n\\nCONCLUSIONS/SIGNIFICANCE: This work identified novel eIF4E alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible eIF4E(S1) allele. Despite high variation present in wild Pisum accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the pea host.", "link"=>"http://www.mendeley.com/research/geographical-gradient-eif4ealleles-conferring-resistance-potyviruses-pea-pisum-germplasm", "reader_count"=>16, "reader_count_by_academic_status"=>{"Researcher"=>6, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>6, "Student > Ph. D. Student"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Japan"=>1}, "group_count"=>0}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/1412387"], "description"=>"<p>Allele designation based on intron 3 length polymorphism, indicating size of obtained fragments with primer combinations A and B, number of repeat motives, intron 3 difference and total length.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "designation", "intron", "fragments", "primer", "combinations"], "article_id"=>955757, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.t001", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_designation_based_on_intron_3_length_polymorphism_indicating_size_of_obtained_fragments_with_primer_combinations_A_and_B_number_of_repeat_motives_intron_3_difference_and_total_length_/955757", "title"=>"Allele designation based on intron 3 length polymorphism, indicating size of obtained fragments with primer combinations A and B, number of repeat motives, intron 3 difference and total length.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412386"], "description"=>"<p>Summary of germplasm screening of 2803 pea accessions, indicating four principal <i>eIF4E</i> intron 3 length variants (A-B-C and S), distribution in total numbers and percentage over 13 geographical regions.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "germplasm", "2803", "pea", "intron", "variants", "numbers", "13", "geographical"], "article_id"=>955756, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_germplasm_screening_of_2803_pea_accessions_indicating_four_principal_eIF4E_intron_3_length_variants_A_B_C_and_S_distribution_in_total_numbers_and_percentage_over_13_geographical_regions_/955756", "title"=>"Summary of germplasm screening of 2803 pea accessions, indicating four principal <i>eIF4E</i> intron 3 length variants (A-B-C and S), distribution in total numbers and percentage over 13 geographical regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412374"], "description"=>"<p>Asterix indicates the position of exchanges previously identified as crucial for resistance.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "amino", "exchanges", "19"], "article_id"=>955751, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summarized_amino_acid_exchanges_of_identified_19_eIF4E_alleles_/955751", "title"=>"Summarized amino acid exchanges of identified 19 <i>eIF4E</i> alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412375"], "description"=>"<p>It is based on total of 156 SNP characters, and excludes 50, 56<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090394#pone-0090394-t001\" target=\"_blank\">Table 1</a>. Red colour of symbols indicates accessions tested resistant to P1 PSbMV. Size of symbols is proportional to number of accessions with given haplotype.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "34", "alleles", "median-joining", "implemented"], "article_id"=>955752, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.g004", "stats"=>{"downloads"=>5, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_network_of_34_alleles_identified_at_eIF4E_whole_gene_level_using_median_joining_network_algorithm_implemented_in_NETWORK_/955752", "title"=>"Haplotype network of 34 alleles identified at <i>eIF4E</i> whole gene level, using median-joining network algorithm, implemented in NETWORK.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412373"], "description"=>"<p>Comparison of allele frequencies in 13 geographical regions, as detailed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090394#pone-0090394-t002\" target=\"_blank\"><b>Table 2</b></a>.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "alleles"], "article_id"=>955750, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographical_distribution_of_four_eIF4E_alleles_expressed_as_percentage_of_total_/955750", "title"=>"Geographical distribution of four <i>eIF4E</i> alleles expressed as percentage of total.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412389", "https://ndownloader.figshare.com/files/1412390"], "description"=>"<div><p>Background</p><p>The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the <i>eIF4E</i> gene to identify novel genetic diversity.</p><p>Methodology/Principal findings</p><p>Germplasm of 2803 pea accessions was screened for <i>eIF4E</i> intron 3 length polymorphism, resulting in the detection of four <i>eIF4E<sup>A-B-C-S</sup></i> variants, whose distribution was geographically structured. The <i>eIF4E<sup>A</sup></i> variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, <i>eIF4E<sup>B</sup></i>, was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The <i>eIF4E<sup>C</sup></i> variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The <i>eIF4E<sup>S</sup></i> variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (<i>eIF4E<sup>A-1-2-3-4-5-6-7</sup></i>, <i>eIF4E<sup>B-1</sup></i>, <i>eIF4E<sup>C-2</sup></i>) conferred resistance to the P1 PSbMV pathotype.</p><p>Conclusions/Significance</p><p>This work identified novel <i>eIF4E</i> alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible <i>eIF4E<sup>S1</sup></i> allele. Despite high variation present in wild <i>Pisum</i> accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the pea host.</p></div>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "geographical", "gradient", "alleles", "conferring", "potyviruses", "pea", "germplasm"], "article_id"=>955759, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0090394.s001", "https://dx.doi.org/10.1371/journal.pone.0090394.s002"], "stats"=>{"downloads"=>5, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Geographical_Gradient_of_the_eIF4E_Alleles_Conferring_Resistance_to_Potyviruses_in_Pea_Pisum_Germplasm/955759", "title"=>"Geographical Gradient of the <i>eIF4E</i> Alleles Conferring Resistance to Potyviruses in Pea (<i>Pisum</i>) Germplasm", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412385"], "description"=>"<p>List of sequenced 73 accessions assigned to identified 19 protein alleles of four <i>eIF4E <sup>A-B-C-S</sup></i> intron 3 length variants with indicated country of origin.</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "sequenced", "73", "accessions", "assigned", "19", "alleles", "intron", "variants", "indicated"], "article_id"=>955755, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_sequenced_73_accessions_assigned_to_identified_19_protein_alleles_of_four_eIF4E_A_B_C_S_intron_3_length_variants_with_indicated_country_of_origin_/955755", "title"=>"List of sequenced 73 accessions assigned to identified 19 protein alleles of four <i>eIF4E <sup>A-B-C-S</sup></i> intron 3 length variants with indicated country of origin.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412384"], "description"=>"<p>Notably, clusters 3 and 4 contain 145 acc. of wild <i>P. fulvum, P. s.</i> subsp. <i>elatius</i> and <i>P. abyssinicum</i>; cluster 7 contains 95 acc. from Afghanistan; cluster 8 has 225 acc. from Ethiopia; and cluster 9 contains 247 acc. from India and Ethiopia, while remaining clusters are more diverse (A). 18 accessions with the <i>eIF4E<sup>A</sup></i> (B), 241 accessions with the <i>eIF4E<sup>B</sup></i> (C), 81 accessions with the <i>eIF4E<sup>C</sup></i> variant (D).</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "variants", "14", "baps", "clusters", "jic", "accessions", "genotyped", "45", "retrotransposon-insertion", "loci"], "article_id"=>955754, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.g005", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_genetic_relationship_of_four_identified_eIF4E_variants_on_the_background_of_14_BAPS_identified_clusters_of_3_029_JIC_accessions_genotyped_by_45_retrotransposon_insertion_loci_13_63_/955754", "title"=>"Visualization of genetic relationship of four identified <i>eIF4E</i> variants on the background of 14 BAPS identified clusters of 3,029 JIC accessions genotyped by 45 retrotransposon-insertion loci [13], [63].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-07 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1412372"], "description"=>"<p>Four principal <i>eIF4E</i> variants identified by intron 3 polymorphism are designated A,B,C and S, while numbers indicate the respective allelic variant. Black bars indicate polymorphism nucleotides within both exons and introns, while red bars indicate polymorphism leading to amino acid exchanges. Horizontal lines indicate insertions/deletions. The heading line indicates nucleotide numbers and exon (solid black boxes)-intron (lines) positions and sizes. Blue arrows indicate primer A combination (Ps-eIF4E-750F and Ps-eIF4E-586gR) and green arrows indicate primer B combination (Ps-eIF4E-750F and Ps-eIF4E-1270R).</p>", "links"=>[], "tags"=>["Agricultural biotechnology", "crops", "Crop diseases", "genetics", "Plant genetics", "Crop genetics", "Plant science", "Agronomy", "Plant breeding", "Plant evolution", "Plant pathology", "alignment", "19"], "article_id"=>955749, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Eva Konečná", "Dana Šafářová", "Milan Navrátil", "Pavel Hanáček", "Clarice Coyne", "Andrew Flavell", "Margarita Vishnyakova", "Mike Ambrose", "Robert Redden", "Petr Smýkal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090394.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_sequence_alignment_of_the_all_19_identified_protein_eIF4E_alleles_/955749", "title"=>"Schematic representation of sequence alignment of the all 19 identified protein <i>eIF4E</i> alleles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-07 03:21:07"}

PMC Usage Stats | Further Information

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Relative Metric

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